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- PDB-9j4g: Crystal structure of SHMT from E. faecium with (+)-SHIN-2 -

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Basic information

Entry
Database: PDB / ID: 9j4g
TitleCrystal structure of SHMT from E. faecium with (+)-SHIN-2
ComponentsSerine hydroxymethyltransferase
KeywordsTRANSFERASE / One carbon metabolism / folate binding
Function / homology
Function and homology information


glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / methyltransferase activity / pyridoxal phosphate binding / methylation / cytosol
Similarity search - Function
Serine hydroxymethyltransferase, pyridoxal phosphate binding site / Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. / : / Serine hydroxymethyltransferase / Serine hydroxymethyltransferase-like domain / Serine hydroxymethyltransferase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
: / Chem-PLS / Serine hydroxymethyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHayashi, H. / Murayama, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP23K07918 Japan
CitationJournal: Arch.Biochem.Biophys. / Year: 2024
Title: SHIN-2 exerts potent activity against VanA-type vancomycin-resistant Enterococcus faecium in vitro by stabilizing the active site loop of serine hydroxymethyltransferase.
Authors: Hayashi, H. / Saijo, E. / Hirata, K. / Murakami, S. / Okuda, H. / Kodama, E.N. / Hasegawa, K. / Murayama, K.
History
DepositionAug 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine hydroxymethyltransferase
B: Serine hydroxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4956
Polymers90,0102
Non-polymers1,4854
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-50 kcal/mol
Surface area27210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.850, 118.850, 162.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Serine hydroxymethyltransferase / SHMT / Serine methylase


Mass: 45005.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria)
Gene: glyA, glyA_1, B1P95_02920, BU183_09275, BU187_13395, BU190_13075, BU192_03790, BXT96_08900, CQR37_06830, CUM68_02790, CUN04_11625, CUS10_03200, CWC53_10155, DKP91_07450, DTPHA_1400422, DTPHA_ ...Gene: glyA, glyA_1, B1P95_02920, BU183_09275, BU187_13395, BU190_13075, BU192_03790, BXT96_08900, CQR37_06830, CUM68_02790, CUN04_11625, CUS10_03200, CWC53_10155, DKP91_07450, DTPHA_1400422, DTPHA_600996, EB12_01905, EfmAA708_21800, F6440_11360, GBM44_11330, GBM73_12625, GJ652_13105, SAMEA3893517_00378
Production host: Escherichia coli (E. coli)
References: UniProt: A0A133CK16, glycine hydroxymethyltransferase
#2: Chemical ChemComp-PLS / [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE / PYRIDOXYL-SERINE-5-MONOPHOSPHATE


Mass: 336.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1L3N / (+)-SHIN-2 / (4~{R})-6-azanyl-4-[3-(hydroxymethyl)-5-(5-oxidanylpent-1-ynyl)phenyl]-3-methyl-4-propan-2-yl-1~{H}-pyrano[2,3-c]pyrazole-5-carbonitrile


Mass: 406.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium cacodylate pH 6.5, 1.26 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→49.39 Å / Num. obs: 85417 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 42.78 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.3
Reflection shellResolution: 1.95→2.07 Å / Num. unique obs: 13775 / CC1/2: 0.602

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V3D

7v3d


Resolution: 1.95→49.39 Å / SU ML: 0.3015 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6899
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2124 2000 2.34 %
Rwork0.1758 83317 -
obs0.1767 85317 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.49 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6251 0 104 491 6846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00846481
X-RAY DIFFRACTIONf_angle_d1.00478798
X-RAY DIFFRACTIONf_chiral_restr0.0538994
X-RAY DIFFRACTIONf_plane_restr0.00731139
X-RAY DIFFRACTIONf_dihedral_angle_d9.3572909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.40431400.36415855X-RAY DIFFRACTION100
2-2.050.32771410.30195872X-RAY DIFFRACTION99.98
2.05-2.110.31521410.27255851X-RAY DIFFRACTION100
2.11-2.180.28521410.24675888X-RAY DIFFRACTION99.98
2.18-2.260.27591410.22815863X-RAY DIFFRACTION99.95
2.26-2.350.2741420.21765897X-RAY DIFFRACTION99.98
2.35-2.460.26651410.21415895X-RAY DIFFRACTION100
2.46-2.590.24541430.19785939X-RAY DIFFRACTION99.98
2.59-2.750.22211420.19525919X-RAY DIFFRACTION99.98
2.75-2.960.23031430.20085957X-RAY DIFFRACTION100
2.96-3.260.23751430.20095951X-RAY DIFFRACTION99.97
3.26-3.730.20191440.16286017X-RAY DIFFRACTION100
3.73-4.70.18491450.12726070X-RAY DIFFRACTION100
4.7-49.390.15491530.1446343X-RAY DIFFRACTION99.95

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